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Exploring alternative patterns of descent

Re-assigning the primary founder

There may be cases where you believe that the primary founder predicted by eBURST is wrong, or where there are two possible founders with substantial bootstrap support and you would like to explore how the eBURST diagram would look if the alternative ST was assigned as the primary founder.

The ability to re-assign the primary founder (see here for details of how to do this) can change the diagram substantially as many STs may be SLVs of both the predicted primary founder and an alternative plausible primary founder, but are preferentially assigned to the primary founder (the true number of SLVs of any ST are shown in the Analysis Window). Re-assigning the primary founder will now preferentially assign all of these SLVs to the user-selected primary founder.

Figure 3 shows an example of an eBURST diagram shown with the primary founder assigned by eBURST (blue) and re-drawn with a user-defined ST as the primary founder (red). The diagrams represent the unedited output of eBURST v2. In this example, the lineage 3 clonal complex of N. meningitidis, we proposed in Feil et al. (2004) that ST303 (arrow) may have been the near extinct founding ST of this large clonal complex, although it is not assigned as the primary founder by eBURST. To explore this further, the diagram is re-drawn with ST303 as the user-defined primary founder, which shows that ST303 has many SLVs and looks a plausible founder. This is also supported by the fact that ST303 has the minimum distance to all other STs in the clonal complex.

Figure 3

An illustrative example is shown in Figure 2. The initial procedure identifies ST1 as the ST with the greatest number of SLVs (the primary founder) and links ST1 to its seven SLVs. It then assigns the SLVs of each of these seven SLVs, and identifies ST2 as a SLV of ST17 and links it. Progressing further outwards, the four descendent SLVs of ST2 are identified and linked, and the process continues outwards and links the four descendent SLVs of ST3. This initial assignment of SLVs from the primary founder outwards results in STs that are SLVs of more than one ST being preferentially assigned to the more centrally positioned ST (ST2 in Figure 2).

In the example shown in Figure 2, optimisation identifies ST10 and ST12 as SLVs of ST3 as well as of ST2. The optimisation procedure re-assigns STs to maximise the numbers of SLVs associated with ST3 as this subgroup founder has more SLVs than ST2 and thus is a more likely subgroup founder. ST2 and ST3 each start with four SLVs and after optimisation ST3 ends up with six linked SLVs (STs 10, 12, 13, 14, 15 and 16) and ST2 with two linked SLVs (STs 3 and 11). Optimisation re-organises the arrangement of STs to maximise the numbers of SLVs associated with subgroup founders, closely approximating the sub-groups produced by the original BURST algorithm, but providing complete linkage between all of the STs in the group.